Variant report

Variant	rs9497403
Chromosome Location	chr6:146054695-146054696
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:146054363-146054703	GM12878	blood:	n/a	chr6:146054529-146054547 chr6:146054531-146054552
2	MAFK	chr6:146054538-146054736	HepG2	liver:	n/a	n/a
3	CEBPB	chr6:146054359-146054707	K562	blood:	n/a	n/a
4	MYC	chr6:146054438-146055284	MCF10A-Er-Src	breast:	n/a	n/a
5	MAFK	chr6:146054613-146054706	HepG2	liver:	n/a	n/a
6	CTCF	chr6:146054441-146055027	K562	blood:	n/a	chr6:146054529-146054547 chr6:146054531-146054552

No.	Distal block	Cell Line	Cell type
1	chr6:146054188..146056153-chr6:146627133..146629580,2	K562	blood:
2	chr6:146051601..146058492-chr6:146282422..146286666,8	K562	blood:
3	chr6:146023773..146025394-chr6:146054656..146056157,2	K562	blood:
4	chr6:146052168..146062191-chr6:146124046..146141258,59	K562	blood:
5	chr6:146047378..146061811-chr6:146118130..146137627,77	K562	blood:

Variant related genes	Relation type
ENSG00000270638	TF binding region
ENSG00000118496	Chromatin interaction
ENSG00000146414	Chromatin interaction
ENSG00000235652	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1011597	0.89[JPT][hapmap]
rs10214925	0.80[ASN][1000 genomes]
rs1055212	0.80[ASN][1000 genomes]
rs1070518	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10872580	0.89[JPT][hapmap]
rs11155438	0.89[JPT][hapmap]
rs12199362	0.89[JPT][hapmap];0.83[YRI][hapmap]
rs1292333	0.89[JPT][hapmap]
rs1292334	0.89[JPT][hapmap]
rs1337841	0.89[JPT][hapmap]
rs1415744	0.89[JPT][hapmap]
rs1415746	0.89[JPT][hapmap]
rs1415747	0.89[JPT][hapmap]
rs1577916	0.80[ASN][1000 genomes]
rs1890170	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1890171	0.89[JPT][hapmap]
rs1970306	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2050027	0.89[JPT][hapmap]
rs2064185	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2142978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2142980	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2206142	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2223411	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2235481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2246132	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2253757	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2265475	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2485631	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34541797	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3811102	0.89[JPT][hapmap];0.83[YRI][hapmap]
rs426371	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4398765	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs455001	0.81[EUR][1000 genomes]
rs4895683	0.89[JPT][hapmap]
rs4896832	0.89[JPT][hapmap]
rs4896837	0.89[JPT][hapmap]
rs4896838	0.92[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4896843	0.80[ASN][1000 genomes]
rs62435775	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6570701	0.89[JPT][hapmap]
rs6570708	0.89[JPT][hapmap]
rs6570732	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs6900175	0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6901888	0.89[JPT][hapmap]
rs6906258	0.89[JPT][hapmap]
rs6906402	0.89[JPT][hapmap]
rs6915718	0.89[JPT][hapmap]
rs6923678	0.80[ASN][1000 genomes]
rs6930154	0.89[JPT][hapmap]
rs6941429	0.89[JPT][hapmap]
rs697053	0.89[JPT][hapmap]
rs697054	0.89[JPT][hapmap]
rs697055	0.89[JPT][hapmap]
rs702304	0.89[JPT][hapmap]
rs702306	0.89[JPT][hapmap]
rs702307	0.89[JPT][hapmap]
rs702316	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs702318	0.92[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs702319	0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs702322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs702324	0.92[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7752286	0.89[JPT][hapmap]
rs7753273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7753770	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs857875	0.89[JPT][hapmap]
rs857877	0.89[JPT][hapmap]
rs857880	0.89[JPT][hapmap]
rs857881	0.89[JPT][hapmap]
rs857882	0.89[JPT][hapmap]
rs857883	0.89[JPT][hapmap]
rs9373467	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9373475	0.89[JPT][hapmap]
rs9376951	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9376961	0.89[JPT][hapmap]
rs9376965	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9386136	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9390356	0.89[JPT][hapmap]
rs9399561	0.89[JPT][hapmap]
rs9403725	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9403737	0.89[JPT][hapmap]
rs9403739	0.92[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9403749	0.83[YRI][hapmap]
rs9485017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9497426	0.83[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3424432	chr6:146041308-146057603	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146026800-146055800	Weak transcription	Left Ventricle	heart
2	chr6:146035800-146055200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:146036200-146054800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:146045000-146055200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:146045600-146054800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:146047800-146055000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:146050000-146055000	Weak transcription	Fetal Lung	lung
8	chr6:146050200-146055000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:146050400-146055600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:146050600-146055000	Weak transcription	Adipose Nuclei	Adipose
11	chr6:146050600-146055000	Weak transcription	Fetal Stomach	stomach
12	chr6:146050600-146055000	Weak transcription	Thymus	Thymus
13	chr6:146050600-146055200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:146050600-146055800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:146050800-146054800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:146050800-146054800	Weak transcription	Brain Germinal Matrix	brain
17	chr6:146050800-146055000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:146050800-146055200	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:146051000-146055000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:146051000-146055600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:146051200-146054800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:146051200-146055000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:146051400-146054800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:146051400-146054800	Weak transcription	HepG2	liver
25	chr6:146051600-146055000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:146052200-146055000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr6:146052400-146054800	Enhancers	Dnd41	blood
28	chr6:146052400-146054800	Enhancers	K562	blood
29	chr6:146052800-146055200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:146052800-146055600	Weak transcription	Aorta	Aorta
31	chr6:146052800-146055600	Weak transcription	Ovary	ovary
32	chr6:146052800-146055800	Weak transcription	Gastric	stomach
33	chr6:146053000-146054800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:146053000-146054800	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr6:146053000-146055000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr6:146053000-146055000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:146053200-146055000	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr6:146053400-146055000	Weak transcription	Fetal Heart	heart
39	chr6:146053800-146055000	Enhancers	Rectal Smooth Muscle	rectum
40	chr6:146054000-146054800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:146054000-146054800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:146054000-146055000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:146054000-146055000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:146054000-146055200	Enhancers	Hela-S3	cervix
45	chr6:146054000-146055200	Enhancers	HUVEC	blood vessel
46	chr6:146054200-146054800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:146054200-146054800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr6:146054200-146055000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:146054200-146055000	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:146054200-146055000	Weak transcription	Psoas Muscle	Psoas

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